/tools/fastx_toolkit/fastx_reverse_complement.xml

 1<tool id="cshl_fastx_reverse_complement" name="Reverse-Complement">
 2	<description></description>
 3	<requirements><requirement type="package">fastx_toolkit</requirement></requirements>
 4	<command>zcat -f '$input' | fastx_reverse_complement -v -o $output
 5#if $input.ext == "fastqsanger":
 6-Q 33
 7#end if
 8	</command>
 9	<inputs>
10		<param format="fasta,fastqsolexa,fastqsanger" name="input" type="data" label="Library to reverse-complement" />
11	</inputs>
12
13	<tests>
14		<test>
15			<!-- Reverse-complement a FASTA file -->
16			<param name="input" value="fastx_rev_comp1.fasta" /> 
17			<output name="output" file="fastx_reverse_complement1.out" />
18		</test>
19		<test>
20			<!-- Reverse-complement a FASTQ file -->
21			<param name="input" value="fastx_rev_comp2.fastq" ftype="fastqsolexa"/>
22			<output name="output" file="fastx_reverse_complement2.out" />
23		</test>
24	</tests>
25
26  
27	<outputs>
28		<data format="input" name="output" metadata_source="input" />
29	</outputs>
30
31<help>
32**What it does**
33
34This tool reverse-complements each sequence in a library.
35If the library is a FASTQ, the quality-scores are also reversed.
36  
37--------
38
39**Example**
40
41Input FASTQ file::
42
43    @CSHL_1_FC42AGWWWXX:8:1:3:740
44    TGTCTGTAGCCTCNTCCTTGTAATTCAAAGNNGGTA
45    +CSHL_1_FC42AGWWWXX:8:1:3:740
46    33 33 33 34 33 33 33 33 33 33 33 33 27 5 27 33 33 33 33 33 33 27 21 27 33 32 31 29 26 24 5 5 15 17 27 26
47
48
49Output FASTQ file::
50
51    @CSHL_1_FC42AGWWWXX:8:1:3:740
52    TACCNNCTTTGAATTACAAGGANGAGGCTACAGACA
53    +CSHL_1_FC42AGWWWXX:8:1:3:740
54    26 27 17 15 5 5 24 26 29 31 32 33 27 21 27 33 33 33 33 33 33 27 5 27 33 33 33 33 33 33 33 33 34 33 33 33
55
56------
57
58This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
59
60 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
61 
62</help>
63</tool>